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- PDB-1tjy: Crystal Structure of Salmonella typhimurium AI-2 receptor LsrB in... -

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Basic information

Entry
Database: PDB / ID: 1tjy
TitleCrystal Structure of Salmonella typhimurium AI-2 receptor LsrB in complex with R-THMF
Componentssugar transport protein
KeywordsSIGNALING PROTEIN / PROTEIN-LIGAND COMPLEX
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Autoinducer 2 ABC transporter, substrate-binding protein LsrB / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PAV / Autoinducer 2-binding protein LsrB / Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMiller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M.
CitationJournal: Mol.Cell / Year: 2004
Title: Salmonella typhimurium Recognizes a Chemically Distinct Form of the Bacterial Quorum-Sensing Signal AI-2
Authors: Miller, S.T. / Xavier, K.B. / Campagna, S.R. / Taga, M.E. / Semmelhack, M.F. / Bassler, B.L. / Hughson, F.M.
History
DepositionJun 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sugar transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4012
Polymers34,2511
Non-polymers1501
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.824, 76.623, 109.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein sugar transport protein


Mass: 34250.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: LsrB / Plasmid: pGEX4-T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8Z2X8, UniProt: Q8ZKQ1*PLUS
#2: Sugar ChemComp-PAV / (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2002
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→63.25 Å / Num. obs: 77033 / % possible obs: 97 % / Rsym value: 0.082 / Net I/σ(I): 9.7
Reflection shellResolution: 1.3→1.334 Å / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→63.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.613 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17156 3863 5 %RANDOM
Rwork0.15563 ---
all0.1578 76855 --
obs0.15643 72992 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.3→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 10 371 2793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222513
X-RAY DIFFRACTIONr_bond_other_d0.0020.022259
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9573416
X-RAY DIFFRACTIONr_angle_other_deg0.97635309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7925315
X-RAY DIFFRACTIONr_chiral_restr0.1020.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022791
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02458
X-RAY DIFFRACTIONr_nbd_refined0.1990.2509
X-RAY DIFFRACTIONr_nbd_other0.2340.22571
X-RAY DIFFRACTIONr_nbtor_other0.0840.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.238
X-RAY DIFFRACTIONr_mcbond_it0.6041.51579
X-RAY DIFFRACTIONr_mcangle_it1.06822558
X-RAY DIFFRACTIONr_scbond_it1.5733934
X-RAY DIFFRACTIONr_scangle_it2.5814.5858
X-RAY DIFFRACTIONr_rigid_bond_restr0.75622513
X-RAY DIFFRACTIONr_sphericity_free1.3252371
X-RAY DIFFRACTIONr_sphericity_bonded1.00722461
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 278
Rwork0.199 4735

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